I have a '00 EX and came upon your same problem when I got an intake.

1) Air temperature sensor (correct me if I'm wrong)
2) Head breather (correct me if I'm wrong)
3) Another breather tube that originates from somewhere in the block

I couldn't just leave that 3rd hose dangling off in space b/c I didn't know what it's purpose was (still don't). So I bought a small head breather, connected that to the head, and used the nipple on the intake for the unidentified hose.

You could do the same thing, for less than $20, or you can drill and attach another nipple on your intake, amount unknown, and just attach all 3 things like they would go on your stock intake.